mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
clean up a couple leaks and some compiler warnings
This commit is contained in:
Greg Landrum
File diff suppressed because it is too large
Load Diff
@@ -42,47 +42,44 @@
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using namespace RDKit;
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void CHECK_RGROUP( RGroupRows::const_iterator &it,
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std::string expected, bool doassert=true ) {
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void CHECK_RGROUP(RGroupRows::const_iterator &it, std::string expected,
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bool doassert = true) {
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std::ostringstream str;
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int i=0;
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int i = 0;
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for(std::map<std::string, boost::shared_ptr<ROMol> >::const_iterator rgroups = it->begin();
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rgroups != it->end();
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++rgroups,++i) {
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if(i) str << " ";
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for (std::map<std::string, boost::shared_ptr<ROMol> >::const_iterator
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rgroups = it->begin();
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rgroups != it->end(); ++rgroups, ++i) {
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if (i) str << " ";
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// rlabel:smiles
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str << rgroups->first << ":" << MolToSmiles(*rgroups->second.get(), true);
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}
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std::string result = str.str();
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if(expected != result) {
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if (expected != result) {
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std::cerr << "Expected: " << expected << std::endl;
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std::cerr << "Got: " << result << std::endl;
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}
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if(doassert)
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TEST_ASSERT(result == expected);
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if (doassert) TEST_ASSERT(result == expected);
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}
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void DUMP_RGROUP( RGroupRows::const_iterator &it,
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std::string result) {
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void DUMP_RGROUP(RGroupRows::const_iterator &it, std::string &result) {
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std::ostringstream str;
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for(std::map<std::string, boost::shared_ptr<ROMol> >::const_iterator rgroups = it->begin();
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rgroups != it->end();
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++rgroups) {
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for (std::map<std::string, boost::shared_ptr<ROMol> >::const_iterator
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rgroups = it->begin();
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rgroups != it->end(); ++rgroups) {
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// rlabel:smiles
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str << rgroups->first << "\t" << MolToSmiles(*rgroups->second.get(), true) << "\t";
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str << rgroups->first << "\t" << MolToSmiles(*rgroups->second.get(), true)
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<< "\t";
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}
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std::cerr << str.str() << std::endl;
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result = str.str();
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}
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const char *symdata[5] = {"c1(Cl)ccccc1",
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"c1c(Cl)cccc1",
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"c1c(Cl)cccc1",
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"c1cc(Cl)ccc1",
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"c1ccc(Cl)cc1"};
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const char *symdata[5] = {"c1(Cl)ccccc1", "c1c(Cl)cccc1", "c1c(Cl)cccc1",
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"c1cc(Cl)ccc1", "c1ccc(Cl)cc1"};
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void testSymmetryMatching() {
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BOOST_LOG(rdInfoLog)
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@@ -91,7 +88,7 @@ void testSymmetryMatching() {
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RWMol *core = SmilesToMol("c1ccccc1");
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RGroupDecomposition decomp(*core);
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for(int i=0; i<5; ++i) {
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for (int i = 0; i < 5; ++i) {
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ROMol *mol = SmilesToMol(symdata[i]);
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int res = decomp.add(*mol);
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TEST_ASSERT(res == i);
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@@ -105,35 +102,34 @@ void testSymmetryMatching() {
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std::ostringstream str;
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// All Cl's should be labeled with the same rgroup
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for(RGroupRows::const_iterator it = rows.begin(); it!=rows.end(); ++it) {
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CHECK_RGROUP( it, "Core:c1ccc([*:1])cc1 R1:Cl[*:1]" );
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for (RGroupRows::const_iterator it = rows.begin(); it != rows.end(); ++it) {
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CHECK_RGROUP(it, "Core:c1ccc([*:1])cc1 R1:Cl[*:1]");
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}
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delete core;
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}
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const char *matchRGroupOnlyData[5] = {"c1(Cl)ccccc1",
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"c1c(Cl)cccc1",
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"c1cc(Cl)ccc1",
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"c1ccc(Cl)cc1",
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"c1c(Cl)cccc(I)1",
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const char *matchRGroupOnlyData[5] = {
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"c1(Cl)ccccc1", "c1c(Cl)cccc1", "c1cc(Cl)ccc1",
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"c1ccc(Cl)cc1", "c1c(Cl)cccc(I)1",
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};
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void testRGroupOnlyMatching() {
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BOOST_LOG(rdInfoLog)
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<< "********************************************************\n";
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BOOST_LOG(rdInfoLog) << "test rgroup decomp rgroup only matching" << std::endl;
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BOOST_LOG(rdInfoLog) << "test rgroup decomp rgroup only matching"
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<< std::endl;
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RWMol *core = SmilesToMol("c1ccccc1[1*]");
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RGroupDecompositionParameters params(IsotopeLabels);
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params.onlyMatchAtRGroups = true;
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RGroupDecomposition decomp(*core, params);
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for(int i=0; i<5; ++i) {
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for (int i = 0; i < 5; ++i) {
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ROMol *mol = SmilesToMol(matchRGroupOnlyData[i]);
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int res = decomp.add(*mol);
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if (i < 4) {
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TEST_ASSERT(res == i);
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}
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else {
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} else {
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TEST_ASSERT(res == -1);
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}
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delete mol;
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@@ -145,22 +141,19 @@ void testRGroupOnlyMatching() {
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std::ostringstream str;
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// All Cl's should be labeled with the same rgroup
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int i=0;
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for(RGroupRows::const_iterator it = rows.begin(); it!=rows.end(); ++it, ++i) {
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CHECK_RGROUP( it, "Core:c1ccc([*:1])cc1 R1:Cl[*:1]" );
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int i = 0;
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for (RGroupRows::const_iterator it = rows.begin(); it != rows.end();
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++it, ++i) {
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CHECK_RGROUP(it, "Core:c1ccc([*:1])cc1 R1:Cl[*:1]");
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}
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delete core;
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}
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const char *ringData[3] = {"c1cocc1",
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"c1c[nH]cc1",
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"c1cscc1"
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};
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const char *ringData[3] = {"c1cocc1", "c1c[nH]cc1", "c1cscc1"};
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const char *ringDataRes[3] = {"Core:c1cc:[*:1]:c1 R1:o(:[*:1]):[*:1]",
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"Core:c1cc:[*:1]:c1 R1:[H]n(:[*:1]):[*:1]",
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"Core:c1cc:[*:1]:c1 R1:s(:[*:1]):[*:1]"
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};
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"Core:c1cc:[*:1]:c1 R1:s(:[*:1]):[*:1]"};
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void testRingMatching() {
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BOOST_LOG(rdInfoLog)
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@@ -169,12 +162,13 @@ void testRingMatching() {
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RWMol *core = SmilesToMol("c1ccc[1*]1");
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RGroupDecompositionParameters params(IsotopeLabels);
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RGroupDecomposition decomp(*core, params);
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for(int i=0; i<3; ++i) {
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for (int i = 0; i < 3; ++i) {
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ROMol *mol = SmilesToMol(ringData[i]);
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int res = decomp.add(*mol);
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TEST_ASSERT(res == i);
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delete mol;
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}
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decomp.process();
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@@ -183,39 +177,37 @@ void testRingMatching() {
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std::ostringstream str;
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// All Cl's should be labeled with the same rgroup
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int i=0;
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for(RGroupRows::const_iterator it = rows.begin(); it!=rows.end(); ++it, ++i) {
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CHECK_RGROUP( it, ringDataRes[i]);
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int i = 0;
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for (RGroupRows::const_iterator it = rows.begin(); it != rows.end();
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++it, ++i) {
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CHECK_RGROUP(it, ringDataRes[i]);
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}
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delete core;
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}
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const char *ringData2[3] = {"c1cocc1CCl",
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"c1c[nH]cc1CI",
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"c1cscc1CF"
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};
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const char *ringData2[3] = {"c1cocc1CCl", "c1c[nH]cc1CI", "c1cscc1CF"};
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const char *ringDataRes2[3] = {
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"Core:[*]1[*][*][*:1](C[*:2])[*]1 R1:[H]c1oc([H])c([*:1])c1[H] R2:Cl[*:2]",
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"Core:[*]1[*][*][*:1](C[*:2])[*]1 R1:[H]c1c([*:1])c([H])n([H])c1[H] R2:I[*:2]",
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"Core:[*]1[*][*][*:1](C[*:2])[*]1 R1:[H]c1sc([H])c([*:1])c1[H] R2:F[*:2]"
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};
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"Core:[*]1[*][*][*:1](C[*:2])[*]1 R1:[H]c1oc([H])c([*:1])c1[H] R2:Cl[*:2]",
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"Core:[*]1[*][*][*:1](C[*:2])[*]1 R1:[H]c1c([*:1])c([H])n([H])c1[H] "
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"R2:I[*:2]",
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"Core:[*]1[*][*][*:1](C[*:2])[*]1 R1:[H]c1sc([H])c([*:1])c1[H] R2:F[*:2]"};
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void testRingMatching2() {
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BOOST_LOG(rdInfoLog)
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<< "********************************************************\n";
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BOOST_LOG(rdInfoLog) << "test rgroup decomp full ring dummy core" << std::endl;
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BOOST_LOG(rdInfoLog) << "test rgroup decomp full ring dummy core"
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<< std::endl;
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RWMol *core = SmartsToMol("*1***[*:1]1C[*:2]");
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RGroupDecompositionParameters params;
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RGroupDecomposition decomp(*core, params);
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for(int i=0; i<3; ++i) {
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for (int i = 0; i < 3; ++i) {
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ROMol *mol = SmilesToMol(ringData2[i]);
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int res = decomp.add(*mol);
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TEST_ASSERT(res == i);
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delete mol;
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}
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decomp.process();
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@@ -223,34 +215,32 @@ void testRingMatching2() {
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std::ostringstream str;
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// All Cl's should be labeled with the same rgroup
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int i=0;
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for(RGroupRows::const_iterator it = rows.begin(); it!=rows.end(); ++it, ++i) {
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CHECK_RGROUP( it, ringDataRes2[i]);
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int i = 0;
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for (RGroupRows::const_iterator it = rows.begin(); it != rows.end();
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++it, ++i) {
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CHECK_RGROUP(it, ringDataRes2[i]);
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}
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delete core;
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}
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const char *ringData3[3] = {"c1cocc1CCl",
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"c1c[nH]cc1CI",
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"c1cscc1CF"
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};
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const char *ringData3[3] = {"c1cocc1CCl", "c1c[nH]cc1CI", "c1cscc1CF"};
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const char *ringDataRes3[3] = {
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"Core:c1co([*:2])cc1[*:1] R1:[H]C([H])(Cl)[*:1]",
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"Core:c1cn([*:2])cc1[*:1] R1:[H]C([H])(I)[*:1] R2:[H][*:2]",
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"Core:c1cs([*:2])cc1[*:1] R1:[H]C([H])(F)[*:1]"
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};
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"Core:c1co([*:2])cc1[*:1] R1:[H]C([H])(Cl)[*:1]",
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"Core:c1cn([*:2])cc1[*:1] R1:[H]C([H])(I)[*:1] R2:[H][*:2]",
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"Core:c1cs([*:2])cc1[*:1] R1:[H]C([H])(F)[*:1]"};
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void testRingMatching3() {
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BOOST_LOG(rdInfoLog)
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<< "********************************************************\n";
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BOOST_LOG(rdInfoLog) << "test rgroup decomp full ring dummy core" << std::endl;
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BOOST_LOG(rdInfoLog) << "test rgroup decomp full ring dummy core"
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<< std::endl;
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RWMol *core = SmartsToMol("*1***[*:1]1");
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RGroupDecompositionParameters params;
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RGroupDecomposition decomp(*core, params);
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for(int i=0; i<3; ++i) {
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for (int i = 0; i < 3; ++i) {
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ROMol *mol = SmilesToMol(ringData3[i]);
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int res = decomp.add(*mol);
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delete mol;
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@@ -263,58 +253,48 @@ void testRingMatching3() {
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std::ostringstream str;
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// All Cl's should be labeled with the same rgroup
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int i=0;
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for(RGroupRows::const_iterator it = rows.begin(); it!=rows.end(); ++it, ++i) {
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CHECK_RGROUP( it, ringDataRes3[i]);
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int i = 0;
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for (RGroupRows::const_iterator it = rows.begin(); it != rows.end();
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++it, ++i) {
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CHECK_RGROUP(it, ringDataRes3[i]);
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}
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delete core;
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}
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const char *coreSmi[] = {
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"C1CCNC(Cl)CC1",
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"C1CC(Cl)NCCC1",
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"C1CCNC(I)CC1",
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"C1CC(I)NCCC1",
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"C1CCSC(Cl)CC1",
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"C1CC(Cl)SCCC1",
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"C1CCSC(I)CC1",
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"C1CC(I)SCCC1",
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"C1CCOC(Cl)CC1",
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"C1CC(Cl)OCCC1",
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"C1CCOC(I)CC1",
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"C1CC(I)OCCC1"
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};
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"C1CCNC(Cl)CC1", "C1CC(Cl)NCCC1", "C1CCNC(I)CC1", "C1CC(I)NCCC1",
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"C1CCSC(Cl)CC1", "C1CC(Cl)SCCC1", "C1CCSC(I)CC1", "C1CC(I)SCCC1",
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"C1CCOC(Cl)CC1", "C1CC(Cl)OCCC1", "C1CCOC(I)CC1", "C1CC(I)OCCC1"};
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const char *coreSmiRes[] = {
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"Core:C1CCC([*:1])N([*:2])CC1 R1:Cl[*:1].[H][*:1] R2:[H][*:2]",
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"Core:C1CCC([*:1])N([*:2])CC1 R1:Cl[*:1].[H][*:1] R2:[H][*:2]",
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"Core:C1CCC([*:1])N([*:2])CC1 R1:I[*:1].[H][*:1] R2:[H][*:2]",
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"Core:C1CCC([*:1])N([*:2])CC1 R1:I[*:1].[H][*:1] R2:[H][*:2]",
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"Core:C1CCSC([*:1])CC1 R1:Cl[*:1].[H][*:1]",
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"Core:C1CCSC([*:1])CC1 R1:Cl[*:1].[H][*:1]",
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"Core:C1CCSC([*:1])CC1 R1:I[*:1].[H][*:1]",
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"Core:C1CCSC([*:1])CC1 R1:I[*:1].[H][*:1]",
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"Core:C1CCOC([*:1])CC1 R1:Cl[*:1].[H][*:1]",
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"Core:C1CCOC([*:1])CC1 R1:Cl[*:1].[H][*:1]",
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"Core:C1CCOC([*:1])CC1 R1:I[*:1].[H][*:1]",
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"Core:C1CCOC([*:1])CC1 R1:I[*:1].[H][*:1]"
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};
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"Core:C1CCC([*:1])N([*:2])CC1 R1:Cl[*:1].[H][*:1] R2:[H][*:2]",
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"Core:C1CCC([*:1])N([*:2])CC1 R1:Cl[*:1].[H][*:1] R2:[H][*:2]",
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"Core:C1CCC([*:1])N([*:2])CC1 R1:I[*:1].[H][*:1] R2:[H][*:2]",
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"Core:C1CCC([*:1])N([*:2])CC1 R1:I[*:1].[H][*:1] R2:[H][*:2]",
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"Core:C1CCSC([*:1])CC1 R1:Cl[*:1].[H][*:1]",
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"Core:C1CCSC([*:1])CC1 R1:Cl[*:1].[H][*:1]",
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"Core:C1CCSC([*:1])CC1 R1:I[*:1].[H][*:1]",
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"Core:C1CCSC([*:1])CC1 R1:I[*:1].[H][*:1]",
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"Core:C1CCOC([*:1])CC1 R1:Cl[*:1].[H][*:1]",
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"Core:C1CCOC([*:1])CC1 R1:Cl[*:1].[H][*:1]",
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"Core:C1CCOC([*:1])CC1 R1:I[*:1].[H][*:1]",
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"Core:C1CCOC([*:1])CC1 R1:I[*:1].[H][*:1]"};
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void testMultiCore() {
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BOOST_LOG(rdInfoLog)
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<< "********************************************************\n";
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BOOST_LOG(rdInfoLog) << "test multi core" << std::endl;
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std::vector<ROMOL_SPTR> cores;
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cores.push_back( ROMOL_SPTR(SmartsToMol("C1CCNCCC1")) );
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cores.push_back( ROMOL_SPTR(SmilesToMol("C1CCOCCC1")) );
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cores.push_back( ROMOL_SPTR(SmilesToMol("C1CCSCCC1")) );
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cores.push_back(ROMOL_SPTR(SmartsToMol("C1CCNCCC1")));
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cores.push_back(ROMOL_SPTR(SmilesToMol("C1CCOCCC1")));
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cores.push_back(ROMOL_SPTR(SmilesToMol("C1CCSCCC1")));
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RGroupDecomposition decomp(cores);
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for(int i=0; i<sizeof(coreSmi)/sizeof(const char *); ++i) {
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for (unsigned int i = 0; i < sizeof(coreSmi) / sizeof(const char *); ++i) {
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ROMol *mol = SmilesToMol(coreSmi[i]);
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int res = decomp.add(*mol);
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unsigned int res = decomp.add(*mol);
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delete mol;
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TEST_ASSERT(res == i);
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}
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@@ -323,10 +303,11 @@ void testMultiCore() {
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RGroupRows rows = decomp.getRGroupsAsRows();
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const RGroupColumns &groups = decomp.getRGroupsAsColumns();
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std::ostringstream str;
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// All Cl's should be labeled with the same rgroup
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int i=0;
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for(RGroupRows::const_iterator it = rows.begin(); it!=rows.end(); ++it, ++i) {
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int i = 0;
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for (RGroupRows::const_iterator it = rows.begin(); it != rows.end();
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++it, ++i) {
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CHECK_RGROUP(it, coreSmiRes[i]);
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}
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}
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